The instability associated with CO2 transport in porous media has a profound impact on geological carbon sequestration. A comprehensive depiction of the CO2 transport at the pore scale is indispensable for a nuanced comprehension of macroscopic processes at the continuum scale. This study integrated the structural features of the HJ saline aquifers in South China Sea with numerical simulations to scrutinize the transport of CO2-brine in porous media. The influences of capillary number (Ca), viscosity ratio (M), and wettability on CO2 phase saturation, phase interface evolution, and fingering phenomena within the pores were meticulously analyzed. The research unveiled that at lower Ca, the transport manifested multiple loosely connected or disconnected finger flow paths. With an increase in the Ca, the fingering pattern evolved from capillary fingering to viscous fingering, resulting in an approximately 42.5% higher CO2 saturation when viscous forces dominate compared to capillary forces. Maintaining a constant injection velocity, the impact of M on transport stability was relatively modest, primarily concentrated in the initial stages of transport. Appropriately decreasing M can enhance CO2 saturation during stable transport. Changes in wettability significantly affected transport stability, CO2 transitioned from dispersed fingering to cluster-driven transport as the medium gradually becomes less hydrophilic, leading to a 44.7% increase in CO2 saturation. This study furnishes theoretical insights for evaluating the efficacy of CO2-brine sequestration and enhancing storage methodologies.